1. LFMM

1.1 Individual sampling

1.1.1 Summary plots

K

walk(K_plots, grid.arrange)

TPRCOMBO

walk(TPR_plots, grid.arrange)

FDRCOMBO

walk(FDR_plots, grid.arrange)

### TOTALN

walk(TOTALN_plots, grid.arrange)

1.1.2 Model summaries

lfmm_ind <- 
  lfmm_ind %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge") %>%
  filter(K_selection == "tracy.widom")
run_lmer(lfmm_ind, "TPRCOMBO", filepath = here(p4path, "LFMM_individual_TPR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp 0.0002 3.8849 3.8849 1 15.3180K 374.16691 2.2 × 10−82***
sampstrat 0.1243 0.8737 0.2912 3 15.3180K 28.04836 4.4 × 10−18***
K 0.0338 4.3713 4.3713 1 15.3180K 421.01179 2.6 × 10−92***
m 0.0358 4.9147 4.9147 1 15.3180K 473.35104 2.2 × 10−103***
phi 0.1114 47.5572 47.5572 1 15.3180K 4580.39346 0.0***
H 0.1150 50.6577 50.6577 1 15.3180K 4879.02098 0.0***
r −0.0183 1.2795 1.2795 1 15.3180K 123.23782 1.6 × 10−28***
*** p < 0.001
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - G −0.0014 0.0023 −0.5948 0.9336946
EG - R 0.0030 0.0023 1.2961 0.5653833
EG - T*** 0.0176 0.0023 7.5567 2.7 × 10−13***
G - R 0.0044 0.0023 1.8908 0.2319131
G - T*** 0.0190 0.0023 8.1508 5.0 × 10−14***
R - T*** 0.0146 0.0023 6.2616 2.3 × 10−9***
*** p < 0.001
run_lmer(lfmm_ind, "FDRCOMBO", filepath = here(p4path, "LFMM_individual_FDR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp −0.0027 549.7338 549.7338 1 15.3180K 3196.9834256 0.0***
sampstrat 0.8382 16.4335 5.4778 3 15.3180K 31.8563530 1.6 × 10−20***
K −0.0468 8.4059 8.4059 1 15.3180K 48.8845389 2.8 × 10−12***
m −0.0687 18.1105 18.1105 1 15.3180K 105.3216241 1.2 × 10−24***
phi −0.0317 3.8567 3.8567 1 15.3180K 22.4287145 2.2 × 10−6***
H 0.0703 18.9143 18.9143 1 15.3180K 109.9965860 1.2 × 10−25***
r −0.0029 0.0324 0.0324 1 15.3180K 0.1886837 0.66
*** p < 0.001
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - G 0.0073 0.0095 0.7712 0.86748324
EG - R*** −0.0253 0.0095 −2.6713 0.03788814***
EG - T** −0.0763 0.0095 −8.0517 5.6 × 10−14**
G - R* −0.0326 0.0095 −3.4424 3.2 × 10−3*
G - T** −0.0836 0.0095 −8.8220 3.0 × 10−14**
R - T** −0.0510 0.0095 −5.3819 4.4 × 10−7**
*** p < 0.05
** p < 0.001
* p < 0.01

1.1.3 Megaplots

MEGAPLOT(lfmm_ind, "K.1", colpal = "turbo")

MEGAPLOT(lfmm_ind, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(lfmm_ind, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(lfmm_ind, "TOTALN", colpal = "viridis")

1.1.4 Latent factor versus sample number test

walk(K_plots, grid.arrange)

walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

walk(TOTALN_plots, grid.arrange)

lfmm_ind_fullK <- 
  lfmm_ind_fullK %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge")
  
run_lmer(lfmm_ind_fullK, "TPRCOMBO", filepath = here(p4path, "LFMM_indfullK_TPR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
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## </style>
##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(&gt;F)</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FCFCFC; color: #000000;">0.0002</td>
## <td class="gt_row gt_right">2.2592</td>
## <td class="gt_row gt_right">2.2592</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">284.911850</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.4 &times; 10<sup class='gt_super'>&minus;63</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0995</td>
## <td class="gt_row gt_right">0.2096</td>
## <td class="gt_row gt_right">0.0699</td>
## <td class="gt_row gt_right">3</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">8.812327</td>
## <td class="gt_row gt_right" style="font-weight: bold;">7.8 &times; 10<sup class='gt_super'>&minus;6</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FEEADA; color: #000000;">0.0231</td>
## <td class="gt_row gt_right">2.0491</td>
## <td class="gt_row gt_right">2.0491</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">258.413832</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;57</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FDD3AB; color: #000000;">0.0550</td>
## <td class="gt_row gt_right">11.5739</td>
## <td class="gt_row gt_right">11.5739</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">1459.604079</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.9 &times; 10<sup class='gt_super'>&minus;305</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FAC088; color: #000000;">0.0796</td>
## <td class="gt_row gt_right">24.2608</td>
## <td class="gt_row gt_right">24.2608</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3059.565188</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FABF85; color: #000000;">0.0814</td>
## <td class="gt_row gt_right">25.3972</td>
## <td class="gt_row gt_right">25.3972</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3202.871668</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #EDEAFD; color: #000000;">&minus;0.0148</td>
## <td class="gt_row gt_right">0.8346</td>
## <td class="gt_row gt_right">0.8346</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">105.249242</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.3 &times; 10<sup class='gt_super'>&minus;24</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
##   </tfoot>
## </table>
## </div>
## 
## [[2]]
## <div id="tpzhtafrqn" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
##   <style>html {
##   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
## }
## 
## #tpzhtafrqn .gt_table {
##   display: table;
##   border-collapse: collapse;
##   margin-left: auto;
##   margin-right: auto;
##   color: #333333;
##   font-size: 16px;
##   font-weight: normal;
##   font-style: normal;
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##   border-top-style: solid;
##   border-top-width: 2px;
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##   border-bottom-color: #A8A8A8;
##   border-left-style: none;
##   border-left-width: 2px;
##   border-left-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_heading {
##   background-color: #FFFFFF;
##   text-align: center;
##   border-bottom-color: #FFFFFF;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
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##   border-right-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_title {
##   color: #333333;
##   font-size: 125%;
##   font-weight: initial;
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## }
## 
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##   font-size: 85%;
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## }
## 
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##   border-bottom-style: solid;
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## }
## 
## #tpzhtafrqn .gt_col_headings {
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##   padding-right: 0;
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## 
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##   border-bottom-style: solid;
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## }
## 
## #tpzhtafrqn .gt_group_heading {
##   padding-top: 8px;
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##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
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## }
## 
## #tpzhtafrqn .gt_empty_group_heading {
##   padding: 0.5px;
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##   background-color: #FFFFFF;
##   font-size: 100%;
##   font-weight: initial;
##   border-top-style: solid;
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##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
##   vertical-align: middle;
## }
## 
## #tpzhtafrqn .gt_from_md > :first-child {
##   margin-top: 0;
## }
## 
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##   margin-bottom: 0;
## }
## 
## #tpzhtafrqn .gt_row {
##   padding-top: 8px;
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##   padding-left: 5px;
##   padding-right: 5px;
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##   border-right-color: #D3D3D3;
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## }
## 
## #tpzhtafrqn .gt_stub {
##   color: #333333;
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## }
## 
## #tpzhtafrqn .gt_stub_row_group {
##   color: #333333;
##   background-color: #FFFFFF;
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## 
## #tpzhtafrqn .gt_row_group_first td {
##   border-top-width: 2px;
## }
## 
## #tpzhtafrqn .gt_summary_row {
##   color: #333333;
##   background-color: #FFFFFF;
##   text-transform: inherit;
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
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## }
## 
## #tpzhtafrqn .gt_first_summary_row {
##   border-top-style: solid;
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## }
## 
## #tpzhtafrqn .gt_first_summary_row.thick {
##   border-top-width: 2px;
## }
## 
## #tpzhtafrqn .gt_last_summary_row {
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_grand_summary_row {
##   color: #333333;
##   background-color: #FFFFFF;
##   text-transform: inherit;
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_first_grand_summary_row {
##   padding-top: 8px;
##   padding-bottom: 8px;
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##   border-top-width: 6px;
##   border-top-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_striped {
##   background-color: rgba(128, 128, 128, 0.05);
## }
## 
## #tpzhtafrqn .gt_table_body {
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
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##   color: #333333;
##   background-color: #FFFFFF;
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##   border-bottom-width: 2px;
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##   border-right-style: none;
##   border-right-width: 2px;
##   border-right-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_footnote {
##   margin: 0px;
##   font-size: 90%;
##   padding-left: 4px;
##   padding-right: 4px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_sourcenotes {
##   color: #333333;
##   background-color: #FFFFFF;
##   border-bottom-style: none;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
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##   border-right-style: none;
##   border-right-width: 2px;
##   border-right-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_sourcenote {
##   font-size: 90%;
##   padding-top: 4px;
##   padding-bottom: 4px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_left {
##   text-align: left;
## }
## 
## #tpzhtafrqn .gt_center {
##   text-align: center;
## }
## 
## #tpzhtafrqn .gt_right {
##   text-align: right;
##   font-variant-numeric: tabular-nums;
## }
## 
## #tpzhtafrqn .gt_font_normal {
##   font-weight: normal;
## }
## 
## #tpzhtafrqn .gt_font_bold {
##   font-weight: bold;
## }
## 
## #tpzhtafrqn .gt_font_italic {
##   font-style: italic;
## }
## 
## #tpzhtafrqn .gt_super {
##   font-size: 65%;
## }
## 
## #tpzhtafrqn .gt_two_val_uncert {
##   display: inline-block;
##   line-height: 1em;
##   text-align: right;
##   font-size: 60%;
##   vertical-align: -0.25em;
##   margin-left: 0.1em;
## }
## 
## #tpzhtafrqn .gt_footnote_marks {
##   font-style: italic;
##   font-weight: normal;
##   font-size: 75%;
##   vertical-align: 0.4em;
## }
## 
## #tpzhtafrqn .gt_asterisk {
##   font-size: 100%;
##   vertical-align: 0;
## }
## 
## #tpzhtafrqn .gt_slash_mark {
##   font-size: 0.7em;
##   line-height: 0.7em;
##   vertical-align: 0.15em;
## }
## 
## #tpzhtafrqn .gt_fraction_numerator {
##   font-size: 0.6em;
##   line-height: 0.6em;
##   vertical-align: 0.45em;
## }
## 
## #tpzhtafrqn .gt_fraction_denominator {
##   font-size: 0.6em;
##   line-height: 0.6em;
##   vertical-align: -0.05em;
## }
## </style>
##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left">EG - G</td>
## <td class="gt_row gt_right" style="background-color: #EAE6FD; color: #000000;">&minus;0.0017</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">&minus;0.8564</td>
## <td class="gt_row gt_right">0.8272429</td></tr>
##     <tr><td class="gt_row gt_left">EG - R</td>
## <td class="gt_row gt_right" style="background-color: #FDF6F0; color: #000000;">0.0008</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">0.3925</td>
## <td class="gt_row gt_right">0.9794972</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - T<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FABF85; color: #000000;">0.0080</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">3.9129</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.3 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left">G - R</td>
## <td class="gt_row gt_right" style="background-color: #FEE8D5; color: #000000;">0.0025</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">1.2489</td>
## <td class="gt_row gt_right">0.5956070</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">G - T<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0097</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">4.7687</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;5</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">R - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC590; color: #000000;">0.0072</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">3.5208</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.4 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p &lt; 0.01</td>
##     </tr>
##   </tfoot>
## </table>
## </div>
run_lmer(lfmm_ind_fullK, "FDRCOMBO", filepath = here(p4path, "LFMM_indfullK_FDR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
## <div id="fixjlqekcp" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
##   <style>html {
##   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
## }
## 
## #fixjlqekcp .gt_table {
##   display: table;
##   border-collapse: collapse;
##   margin-left: auto;
##   margin-right: auto;
##   color: #333333;
##   font-size: 16px;
##   font-weight: normal;
##   font-style: normal;
##   background-color: #FFFFFF;
##   width: auto;
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #A8A8A8;
##   border-right-style: none;
##   border-right-width: 2px;
##   border-right-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #A8A8A8;
##   border-left-style: none;
##   border-left-width: 2px;
##   border-left-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_heading {
##   background-color: #FFFFFF;
##   text-align: center;
##   border-bottom-color: #FFFFFF;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
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## 
## #fixjlqekcp .gt_title {
##   color: #333333;
##   font-size: 125%;
##   font-weight: initial;
##   padding-top: 4px;
##   padding-bottom: 4px;
##   padding-left: 5px;
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##   border-bottom-color: #FFFFFF;
##   border-bottom-width: 0;
## }
## 
## #fixjlqekcp .gt_subtitle {
##   color: #333333;
##   font-size: 85%;
##   font-weight: initial;
##   padding-top: 0;
##   padding-bottom: 6px;
##   padding-left: 5px;
##   padding-right: 5px;
##   border-top-color: #FFFFFF;
##   border-top-width: 0;
## }
## 
## #fixjlqekcp .gt_bottom_border {
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_col_headings {
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_col_heading {
##   color: #333333;
##   background-color: #FFFFFF;
##   font-size: 100%;
##   font-weight: normal;
##   text-transform: inherit;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
##   vertical-align: bottom;
##   padding-top: 5px;
##   padding-bottom: 6px;
##   padding-left: 5px;
##   padding-right: 5px;
##   overflow-x: hidden;
## }
## 
## #fixjlqekcp .gt_column_spanner_outer {
##   color: #333333;
##   background-color: #FFFFFF;
##   font-size: 100%;
##   font-weight: normal;
##   text-transform: inherit;
##   padding-top: 0;
##   padding-bottom: 0;
##   padding-left: 4px;
##   padding-right: 4px;
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##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
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##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFC; color: #000000;">&minus;0.0025</td>
## <td class="gt_row gt_right">501.9981</td>
## <td class="gt_row gt_right">501.9981</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3776.700755</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.5655</td>
## <td class="gt_row gt_right">14.8749</td>
## <td class="gt_row gt_right">4.9583</td>
## <td class="gt_row gt_right">3</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">37.302920</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.2 &times; 10<sup class='gt_super'>&minus;24</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FDF9F6; color: #000000;">0.0220</td>
## <td class="gt_row gt_right">1.8480</td>
## <td class="gt_row gt_right">1.8480</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">13.902783</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.9 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FEF2E9; color: #000000;">0.0711</td>
## <td class="gt_row gt_right">19.3767</td>
## <td class="gt_row gt_right">19.3767</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">145.777616</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.1 &times; 10<sup class='gt_super'>&minus;33</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #F6F5FC; color: #000000;">&minus;0.0329</td>
## <td class="gt_row gt_right">4.1374</td>
## <td class="gt_row gt_right">4.1374</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">31.127031</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.5 &times; 10<sup class='gt_super'>&minus;8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FEEFE2; color: #000000;">0.0974</td>
## <td class="gt_row gt_right">36.3261</td>
## <td class="gt_row gt_right">36.3261</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">273.293640</td>
## <td class="gt_row gt_right" style="font-weight: bold;">7.3 &times; 10<sup class='gt_super'>&minus;61</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #FAF9FC; color: #000000;">&minus;0.0122</td>
## <td class="gt_row gt_right">0.5737</td>
## <td class="gt_row gt_right">0.5737</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">4.316443</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.038<sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
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##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left">EG - G</td>
## <td class="gt_row gt_right" style="background-color: #FCFAF7; color: #000000;">0.0024</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">0.2905</td>
## <td class="gt_row gt_right">0.991466</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - R<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #D2CCFD; color: #000000;">&minus;0.0306</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;3.6725</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.4 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #8C8AFC; color: #000000;">&minus;0.0748</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;8.9768</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.7 &times; 10<sup class='gt_super'>&minus;14</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">G - R<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #CFC8FD; color: #000000;">&minus;0.0330</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;3.9628</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.3 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">G - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #8787FC; color: #000000;">&minus;0.0772</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;9.2667</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.3 &times; 10<sup class='gt_super'>&minus;14</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">R - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #BEB7FD; color: #000000;">&minus;0.0442</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;5.3064</td>
## <td class="gt_row gt_right" style="font-weight: bold;">6.7 &times; 10<sup class='gt_super'>&minus;7</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.01</td>
##     </tr>
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p &lt; 0.001</td>
##     </tr>
##   </tfoot>
## </table>
## </div>

1.2 Site sampling

1.2.1 Summary plots

K

walk(K_plots, grid.arrange)

TPRCOMBO

walk(TPR_plots, grid.arrange)

FDRCOMBO

walk(FDR_plots, grid.arrange)

TOTALN

walk(TOTALN_plots, grid.arrange)

1.1.2 Model summaries

lfmm_site <- 
  lfmm_site %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge") %>%
  filter(K_selection == "tracy.widom")
run_lmer(lfmm_site, "TPRCOMBO", filepath = here(p4path, "LFMM_site_TPR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp −0.0004 0.0593 0.0593 1 8.6090K 8.070827 4.5 × 10−3***
sampstrat 0.0362 0.1180 0.0590 2 8.6090K 8.023909 3.3 × 10−4**
K 0.0160 0.5507 0.5507 1 8.6090K 74.893340 5.9 × 10−18**
m 0.0417 3.7529 3.7529 1 8.6090K 510.419793 7.7 × 10−110**
phi 0.0536 6.1900 6.1900 1 8.6090K 841.869068 1.1 × 10−176**
H 0.0741 11.8217 11.8217 1 8.6090K 1607.807275 1.7 × 10−322**
r −0.0213 0.9766 0.9766 1 8.6090K 132.822293 1.7 × 10−30**
*** p < 0.01
** p < 0.001
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - EQ 0.0043 0.0023 1.8813 0.14407422
EG - R*** 0.0091 0.0023 4.0035 1.8 × 10−4***
EQ - R 0.0048 0.0023 2.1241 0.08499688
*** p < 0.001
run_lmer(lfmm_site, "FDRCOMBO", filepath = here(p4path, "LFMM_site_FDR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp −0.0083 25.3129 25.3129 1 8.6110K 842.37960203 8.7 × 10−177***
sampstrat 1.0906 0.0540 0.0270 2 8.6110K 0.89778252 0.410
K 0.0096 0.1966 0.1966 1 8.6110K 6.54282626 0.011**
m 0.0161 0.5617 0.5617 1 8.6110K 18.69390804 1.6 × 10−5***
phi −0.0238 1.2192 1.2192 1 8.6110K 40.57304948 2.0 × 10−10***
H 0.0009 0.0018 0.0018 1 8.6110K 0.06058928 0.810
r 0.0036 0.0281 0.0281 1 8.6110K 0.93373450 0.330
*** p < 0.001
** p < 0.05
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - EQ −0.0061 0.0046 −1.3303 0.3782653
EG - R −0.0024 0.0046 −0.5263 0.8584367
EQ - R 0.0037 0.0046 0.8037 0.7007541

1.2.3 Megaplots

MEGAPLOT(lfmm_site, "K.1", colpal = "turbo")

MEGAPLOT(lfmm_site, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(lfmm_site, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(lfmm_site, "TOTALN", colpal = "viridis")

1.2.4 Latent factor versus sample number test

walk(K_plots, grid.arrange)

walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

walk(TOTALN_plots, grid.arrange) 

lfmm_site_fullK <- 
  lfmm_site_fullK %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge")
  
run_lmer(lfmm_site_fullK, "TPRCOMBO", filepath = here(p4path, "LFMM_sitefullK_TPR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
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##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(&gt;F)</th>
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##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #F9F9FC; color: #000000;">&minus;0.0018</td>
## <td class="gt_row gt_right">1.1952</td>
## <td class="gt_row gt_right">1.1952</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">183.240394</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.5 &times; 10<sup class='gt_super'>&minus;41</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #FEE6D1; color: #000000;">0.0191</td>
## <td class="gt_row gt_right">0.0892</td>
## <td class="gt_row gt_right">0.0446</td>
## <td class="gt_row gt_right">2</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">6.835991</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FEEBDA; color: #000000;">0.0152</td>
## <td class="gt_row gt_right">0.4970</td>
## <td class="gt_row gt_right">0.4970</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">76.192821</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.1 &times; 10<sup class='gt_super'>&minus;18</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FDD0A5; color: #000000;">0.0389</td>
## <td class="gt_row gt_right">3.2589</td>
## <td class="gt_row gt_right">3.2589</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">499.649532</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.3 &times; 10<sup class='gt_super'>&minus;107</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FCCA9A; color: #000000;">0.0442</td>
## <td class="gt_row gt_right">4.2123</td>
## <td class="gt_row gt_right">4.2123</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">645.825647</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.9 &times; 10<sup class='gt_super'>&minus;137</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0656</td>
## <td class="gt_row gt_right">9.2807</td>
## <td class="gt_row gt_right">9.2807</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1422.900812</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.6 &times; 10<sup class='gt_super'>&minus;288</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #DBD6FD; color: #000000;">&minus;0.0206</td>
## <td class="gt_row gt_right">0.9155</td>
## <td class="gt_row gt_right">0.9155</td>
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## <td class="gt_row gt_right">140.355642</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.0 &times; 10<sup class='gt_super'>&minus;32</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
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##   <table class="gt_table">
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##     <tr>
##       <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - EQ<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC48F; color: #000000;">0.0057</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">2.6691</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.02077436<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - R<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0076</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">3.5508</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left">EQ - R</td>
## <td class="gt_row gt_right" style="background-color: #FEE9D7; color: #000000;">0.0019</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">0.8835</td>
## <td class="gt_row gt_right">0.65075396</td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.05</td>
##     </tr>
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p &lt; 0.01</td>
##     </tr>
##   </tfoot>
## </table>
## </div>
run_lmer(lfmm_site_fullK, "FDRCOMBO", filepath = here(p4path, "LFMM_sitefullK_FDR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
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##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(&gt;F)</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FAFAFC; color: #000000;">&minus;0.0187</td>
## <td class="gt_row gt_right">129.4249</td>
## <td class="gt_row gt_right">129.4249</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1992.658631</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">1.2219</td>
## <td class="gt_row gt_right">2.3866</td>
## <td class="gt_row gt_right">1.1933</td>
## <td class="gt_row gt_right">2</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">18.372105</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFA; color: #000000;">0.0190</td>
## <td class="gt_row gt_right">0.7755</td>
## <td class="gt_row gt_right">0.7755</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">11.939477</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.5 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFA; color: #000000;">0.0196</td>
## <td class="gt_row gt_right">0.8298</td>
## <td class="gt_row gt_right">0.8298</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">12.776418</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.5 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FAFAFC; color: #000000;">&minus;0.0191</td>
## <td class="gt_row gt_right">0.7830</td>
## <td class="gt_row gt_right">0.7830</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">12.054888</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.2 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FCFAF7; color: #000000;">0.0389</td>
## <td class="gt_row gt_right">3.2570</td>
## <td class="gt_row gt_right">3.2570</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">50.145685</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.5 &times; 10<sup class='gt_super'>&minus;12</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left">r</td>
## <td class="gt_row gt_right" style="background-color: #FCFCFB; color: #000000;">0.0065</td>
## <td class="gt_row gt_right">0.0916</td>
## <td class="gt_row gt_right">0.0916</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1.410227</td>
## <td class="gt_row gt_right">0.24</td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
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## </table>
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##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
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##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
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##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - EQ<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC28B; color: #000000;">0.0301</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">4.4781</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.2 &times; 10<sup class='gt_super'>&minus;5</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left">EG - R</td>
## <td class="gt_row gt_right" style="background-color: #E5E1FD; color: #000000;">&minus;0.0087</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">&minus;1.2978</td>
## <td class="gt_row gt_right">0.396384</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EQ - R<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #8787FC; color: #000000;">&minus;0.0388</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">&minus;5.7761</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.3 &times; 10<sup class='gt_super'>&minus;8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
##   </tfoot>
## </table>
## </div>

2. RDA

2.1 Individual sampling

2.1.1 Summary plots

rda_ind <- format_rda(here(p3path, "rda_indsampling_results.csv"))
rda_ind_tidy <- 
  rda_ind %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  group_by(correctPC) %>%
  group_split()
walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

2.1.2 Model summaries

rda_ind <- 
  rda_ind %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(correctPC == "FALSE") 
run_lmer(rda_ind, "TPRCOMBO", filepath = here(p4path, "RDA_individual_TPR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp 0.0002 2.8394 2.8394 1 15.3480K 545.389450 1.5 × 10−118***
sampstrat 0.0875 0.3001 0.1000 3 15.3480K 19.211563 2.0 × 10−12***
K 0.0165 1.0439 1.0439 1 15.3480K 200.509665 3.1 × 10−45***
m 0.0438 7.3555 7.3555 1 15.3480K 1412.856406 7.2 × 10−296***
phi 0.0440 7.4213 7.4213 1 15.3480K 1425.494641 2.2 × 10−298***
H 0.0436 7.2900 7.2900 1 15.3480K 1400.274445 2.3 × 10−293***
r 0.0036 0.0488 0.0488 1 15.3480K 9.371404 2.2 × 10−3**
*** p < 0.001
** p < 0.01
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - G 0.0005 0.0016 0.2768 0.9926010
EG - R 0.0029 0.0016 1.7594 0.2931233
EG - T*** 0.0110 0.0016 6.6817 1.4 × 10−10***
G - R 0.0024 0.0016 1.4826 0.4480091
G - T*** 0.0105 0.0016 6.4050 9.0 × 10−10***
R - T*** 0.0081 0.0016 4.9224 5.1 × 10−6***
*** p < 0.001
run_lmer(rda_ind, "FDRCOMBO", filepath = here(p4path, "RDA_individual_FDR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp 0.0003 5.7961 5.7961 1 15.3480K 373.268676 3.4 × 10−82***
sampstrat 0.1162 0.2103 0.0701 3 15.3480K 4.515102 3.6 × 10−3**
K 0.0153 0.9004 0.9004 1 15.3480K 57.987784 2.8 × 10−14***
m 0.0753 21.8007 21.8007 1 15.3480K 1403.969867 4.2 × 10−294***
phi 0.0647 16.0600 16.0600 1 15.3480K 1034.264854 1.2 × 10−219***
H 0.0610 14.2799 14.2799 1 15.3480K 919.628150 3.1 × 10−196***
r 0.0091 0.3176 0.3176 1 15.3480K 20.451012 6.2 × 10−6***
*** p < 0.001
** p < 0.01
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - G −0.0010 0.0028 −0.3555 0.98460216
EG - R 0.0020 0.0028 0.6959 0.89870855
EG - T*** 0.0085 0.0028 2.9888 0.01487071***
G - R 0.0030 0.0028 1.0514 0.71907362
G - T** 0.0095 0.0028 3.3443 4.6 × 10−3**
R - T 0.0065 0.0028 2.2929 0.09963697
*** p < 0.05
** p < 0.01

1.1.3 Megaplots

MEGAPLOT(rda_ind, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(rda_ind, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(rda_ind, "TOTALN", colpal = "viridis")

2.2 Site sampling

2.2.1 Summary plots

rda_site <- format_rda(here(p3path, "rda_sitesampling_results.csv")) 
rda_site_tidy <- 
  rda_site %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  group_by(correctPC) %>%
  group_split()
walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

walk(TOTALN_plots, grid.arrange)

2.2.2 Model summaries

rda_site <- 
  rda_site %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(correctPC == "FALSE") 
run_lmer(rda_site, "TPRCOMBO", filepath = here(p4path, "RDA_site_TPR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp 0.0015 0.8335 0.8335 1 8.6290K 232.154396 9.5 × 10−52***
sampstrat 0.0717 0.1133 0.0567 2 8.6290K 15.782322 1.4 × 10−7***
K 0.0173 0.6489 0.6489 1 8.6290K 180.732574 8.6 × 10−41***
m 0.0322 2.2403 2.2403 1 8.6290K 623.983518 5.0 × 10−133***
phi 0.0321 2.2322 2.2322 1 8.6290K 621.743005 1.4 × 10−132***
H 0.0315 2.1447 2.1447 1 8.6290K 597.363316 1.3 × 10−127***
r 0.0019 0.0081 0.0081 1 8.6290K 2.261166 0.13
*** p < 0.001
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - EQ −0.0001 0.0016 −0.0550 0.9983351
EG - R*** 0.0076 0.0016 4.8378 3.9 × 10−6***
EQ - R*** 0.0077 0.0016 4.8928 3.0 × 10−6***
*** p < 0.001
run_lmer(rda_site, "FDRCOMBO", filepath = here(p4path, "RDA_site_FDR.csv"))
[[1]]
Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors Fixed Effects Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
nsamp 0.0018 1.1681 1.1681 1 8.6290K 140.00975 4.7 × 10−32***
sampstrat 0.0845 0.1085 0.0542 2 8.6290K 6.50242 1.5 × 10−3**
K 0.0133 0.3801 0.3801 1 8.6290K 45.55864 1.6 × 10−11***
m 0.0378 3.0791 3.0791 1 8.6290K 369.07182 1.4 × 10−80***
phi 0.0336 2.4370 2.4370 1 8.6290K 292.10683 2.0 × 10−64***
H 0.0297 1.8994 1.8994 1 8.6290K 227.67214 8.5 × 10−51***
r 0.0144 0.4449 0.4449 1 8.6290K 53.32587 3.1 × 10−13***
*** p < 0.001
** p < 0.01
[[2]]
Tukey test
pairwise ~ sampstrat
Contrast Estimate SE Z ratio p
EG - EQ*** 0.0057 0.0024 2.3728 0.04642683***
EG - R** 0.0085 0.0024 3.5382 1.2 × 10−3**
EQ - R 0.0028 0.0024 1.1654 0.47395300
*** p < 0.05
** p < 0.01

2.2.3 Megaplots

MEGAPLOT(rda_site, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(rda_site, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(rda_site, "TOTALN", colpal = "viridis")

Figures

arrange_figures(lfmm_ind, rda_ind, "FDR", 
                "A. LFMM", "B. RDA",
                colpal = "viridis", direction = -1, dig = 2, maxv = 0.86, minv = 0)

arrange_figures(lfmm_ind, rda_ind, "TPR", 
                "A. LFMM", "B. RDA",
                colpal = "plasma", direction = 1, dig = 2, minv = 0, maxv = 0.17)

arrange_figures(lfmm_site, rda_site, "TPR", 
                "A. LFMM", "B. RDA",
                colpal = "plasma", direction = 1, dig = 2, minv = 0, maxv = 0.11)

arrange_figures(lfmm_site, rda_site, "FDR", 
                "A. LFMM", "B. RDA",
                colpal = "viridis", direction = -1, dig = 2, maxv = 1, minv = 0)